We present detailed profiles of vertical water flux from the surface to 1.2 m beneath the Haughton River in the tropical northeast of Australia. A 1-D numerical model is used to estimate vertical flux based on raw temperature time series observations from within downwelling, upwelling, neutral, and convergent sections of the hyporheic zone. A Monte Carlo analysis is used to derive error bounds for the fluxes based on temperature measurement error and uncertainty in effective thermal diffusivity. Vertical fluxes ranged from 5.7 m d-1 (downward) to -0.2 m d-1 (upward) with the lowest relative errors for values between 0.3 and 6 m d-1. Our 1-D approach provides a useful alternative to 1-D analytical and other solutions because it does not incorporate errors associated with simplified boundary conditions or assumptions of purely vertical flow, hydraulic parameter values, or hydraulic conditions. To validate the ability of this 1-D approach to represent the vertical fluxes of 2-D flow fields, we compare our model with two simple 2-D flow fields using a commercial numerical model. These comparisons showed that: (1) the 1-D vertical flux was equivalent to the mean vertical component of flux irrespective of a changing horizontal flux; and (2) the subsurface temperature data inherently has a "spatial footprint" when the vertical flux profiles vary spatially. Thus, the mean vertical flux within a 2-D flow field can be estimated accurately without requiring the flow to be purely vertical. The temperature-derived 1-D vertical flux represents the integrated vertical component of flux along the flow path intersecting the observation point. Key Points Temperature signals at depth represent the mean vertical flux along a flow path Magnitude of vertical flux decreases with depth through the hyporheic zone Vertical fluxes have an effective "spatial footprint"